29527 add sequencing facility (#205)

* 29527 Add Sequencing Facility
Added db migration + entity + crud test

* 29527 Add Sequencing Facility
Added dto and repository

* 29527 Add Sequencing Facility
Added Open API specs testing

src/main/java/ca/gc/aafc/seqdb/api/dto/SequencingFacilityDto.java

@@ -0,0 +1,37 @@
+package ca.gc.aafc.seqdb.api.dto;
+
+import ca.gc.aafc.dina.dto.RelatedEntity;
+import ca.gc.aafc.seqdb.api.entities.SequencingFacility;
+import io.crnk.core.resource.annotations.JsonApiId;
+import io.crnk.core.resource.annotations.JsonApiResource;
+import lombok.Data;
+import org.javers.core.metamodel.annotation.Id;
+import org.javers.core.metamodel.annotation.PropertyName;
+import org.javers.core.metamodel.annotation.TypeName;
+
+import java.time.OffsetDateTime;
+import java.util.List;
+import java.util.UUID;
+
+@Data
+@JsonApiResource(type = SequencingFacilityDto.TYPENAME)
+@RelatedEntity(SequencingFacility.class)
+@TypeName(SequencingFacilityDto.TYPENAME)
+public class SequencingFacilityDto {
+
+  public static final String TYPENAME = "sequencing-facility";
+
+  @JsonApiId
+  @Id
+  @PropertyName("id")
+  private UUID uuid;
+
+  private String createdBy;
+  private OffsetDateTime createdOn;
+  private String group;
+  private String name;
+
+  private List<SequencingFacility.ContactRole> contacts = List.of();
+  private SequencingFacility.Address shippingAddress;
+
+}

src/main/java/ca/gc/aafc/seqdb/api/entities/SequencingFacility.java

@@ -0,0 +1,113 @@
+package ca.gc.aafc.seqdb.api.entities;
+
+import ca.gc.aafc.dina.entity.DinaEntity;
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.RequiredArgsConstructor;
+import org.hibernate.annotations.Generated;
+import org.hibernate.annotations.GenerationTime;
+import org.hibernate.annotations.NaturalId;
+import org.hibernate.annotations.NaturalIdCache;
+import org.hibernate.annotations.Type;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import javax.validation.Valid;
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotEmpty;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
+import java.time.OffsetDateTime;
+import java.util.List;
+import java.util.UUID;
+
+@Entity
+@Data
+@AllArgsConstructor
+@RequiredArgsConstructor
+@Builder
+@NaturalIdCache
+@Table(name = "sequencing_facility")
+public class SequencingFacility implements DinaEntity {
+
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  private Integer id;
+
+  @NaturalId
+  @NotNull
+  @Column(unique = true)
+  private UUID uuid;
+
+  @NotBlank
+  @Column(name = "created_by", updatable = false)
+  private String createdBy;
+
+  @Column(name = "created_on", insertable = false, updatable = false)
+  @Generated(value = GenerationTime.INSERT)
+  private OffsetDateTime createdOn;
+
+  @NotBlank
+  @Size(max = 50)
+  @Column(name = "_group")
+  private String group;
+
+  @NotBlank
+  @Size(max = 50)
+  private String name;
+
+  @Type(type = "jsonb")
+  @Column(name = "contacts", columnDefinition = "jsonb")
+  @Valid
+  private List<ContactRole> contacts = List.of();
+
+  @Type(type = "jsonb")
+  @Column(name = "shipping_address", columnDefinition = "jsonb")
+  @Valid
+  private Address shippingAddress;
+
+  @Data
+  @Builder
+  public static class ContactRole {
+
+    @NotEmpty
+    private String name;
+
+    @NotEmpty
+    private List<@NotBlank String> roles;
+
+    @Size(max = 100)
+    private String info;
+
+  }
+
+  // TODO to be replaced by dina-base-api version in 0.99
+  @Data
+  @Builder
+  public static class Address {
+
+    @Size (max = 150)
+    private String addressLine1;
+
+    @Size (max = 150)
+    private String addressLine2;
+
+    @Size (max = 150)
+    private String city;
+
+    @Size (max = 150)
+    private String provinceState;
+
+    @Size (max = 50)
+    private String zipCode;
+
+    @Size (max = 50)
+    private String country;
+
+  }
+}

src/main/java/ca/gc/aafc/seqdb/api/repository/SequencingFacilityRepository.java

@@ -0,0 +1,37 @@
+package ca.gc.aafc.seqdb.api.repository;
+
+import ca.gc.aafc.dina.mapper.DinaMapper;
+import ca.gc.aafc.dina.repository.DinaRepository;
+import ca.gc.aafc.dina.repository.external.ExternalResourceProvider;
+import ca.gc.aafc.dina.security.DinaAuthorizationService;
+import ca.gc.aafc.dina.service.DinaService;
+import ca.gc.aafc.seqdb.api.dto.SequencingFacilityDto;
+import ca.gc.aafc.seqdb.api.entities.SequencingFacility;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import lombok.NonNull;
+import org.springframework.boot.info.BuildProperties;
+import org.springframework.stereotype.Repository;
+
+import java.util.Optional;
+
+@Repository
+public class SequencingFacilityRepository extends DinaRepository<SequencingFacilityDto, SequencingFacility> {
+
+  public SequencingFacilityRepository(
+          @NonNull DinaService<SequencingFacility> dinaService,
+          DinaAuthorizationService groupAuthorizationService,
+          @NonNull BuildProperties props,
+          ExternalResourceProvider externalResourceProvider,
+          ObjectMapper objMapper) {
+    super(
+            dinaService,
+            groupAuthorizationService,
+            Optional.empty(),
+            new DinaMapper<>(SequencingFacilityDto.class),
+            SequencingFacilityDto.class, SequencingFacility.class,
+            null,
+            externalResourceProvider,
+            props, objMapper);
+  }
+
+}

src/main/java/ca/gc/aafc/seqdb/api/service/SequencingFacilityService.java

@@ -0,0 +1,27 @@
+package ca.gc.aafc.seqdb.api.service;
+
+import ca.gc.aafc.dina.jpa.BaseDAO;
+import ca.gc.aafc.dina.service.DefaultDinaService;
+
+import ca.gc.aafc.seqdb.api.entities.SequencingFacility;
+import lombok.NonNull;
+import org.springframework.stereotype.Service;
+import org.springframework.validation.SmartValidator;
+
+import java.util.UUID;
+
+@Service
+public class SequencingFacilityService extends DefaultDinaService<SequencingFacility> {
+
+  public SequencingFacilityService(
+          @NonNull BaseDAO baseDAO,
+          @NonNull SmartValidator sv) {
+    super(baseDAO, sv);
+  }
+
+  @Override
+  protected void preCreate(SequencingFacility entity) {
+    entity.setUuid(UUID.randomUUID());
+  }
+}
+

src/main/resources/db/changelog/db.changelog-master.xml

@@ -36,4 +36,5 @@
   <include file="db/changelog/migrations/29-Replace_thermocycler_profile_steps_by_an_array.xml"/>
   <include file="db/changelog/migrations/30-Allow_storage_unit_type_on_pcrbatch.xml"/>
   <include file="db/changelog/migrations/31-Add_reaction_date_to_seqbatch.xml"/>
+  <include file="db/changelog/migrations/32-Add_sequencing_facility.xml"/>
 </databaseChangeLog>

src/main/resources/db/changelog/migrations/32-Add_sequencing_facility.xml

@@ -0,0 +1,29 @@
+<?xml version="1.1" encoding="UTF-8" standalone="no"?>
+<databaseChangeLog
+        xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+        xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog https://local.xsd/dbchangelog-4.4.xsd"
+        objectQuotingStrategy="QUOTE_ONLY_RESERVED_WORDS">
+    <changeSet id="32-Create_Sequencing_Facility" context="schema-change" author="cgendreau">
+        <createTable tableName="sequencing_facility">
+            <column autoIncrement="true" name="id" type="SERIAL">
+                <constraints primaryKey="true" primaryKeyName="pk_sequencing_facility_id" />
+            </column>
+            <column name="uuid" type="uuid">
+                <constraints nullable="false" unique="true" />
+            </column>
+            <column name="created_by" type="VARCHAR(250)">
+                <constraints nullable="false"/>
+            </column>
+            <column name="_group" type="VARCHAR(50)">
+                <constraints nullable="false"/>
+            </column>
+            <column name="created_on" type="timestamptz" defaultValueComputed="current_timestamp"/>
+            <column name="name" type="VARCHAR(50)">
+                <constraints nullable="false"/>
+            </column>
+            <column name="shipping_address" type="jsonb"/>
+            <column name="contacts" type="jsonb"/>
+        </createTable>
+    </changeSet>
+</databaseChangeLog>

src/test/java/ca/gc/aafc/seqdb/api/SequenceModuleBaseIT.java

@@ -4,6 +4,7 @@
 
 import ca.gc.aafc.seqdb.api.service.PcrBatchItemService;
 import ca.gc.aafc.seqdb.api.service.SeqSubmissionService;
+import ca.gc.aafc.seqdb.api.service.SequencingFacilityService;
 
 public class SequenceModuleBaseIT extends BaseIntegrationTest {
 
@@ -12,5 +13,8 @@ public class SequenceModuleBaseIT extends BaseIntegrationTest {
 
   @Inject 
   protected SeqSubmissionService seqSubmissionService;
+
+  @Inject
+  protected SequencingFacilityService sequencingFacilityService;
 
 }

src/test/java/ca/gc/aafc/seqdb/api/entities/SequenceFacilityCRUDIT.java

@@ -0,0 +1,46 @@
+package ca.gc.aafc.seqdb.api.entities;
+
+import ca.gc.aafc.seqdb.api.SequenceModuleBaseIT;
+import ca.gc.aafc.seqdb.api.testsupport.factories.SequencingFacilityFactory;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+
+public class SequenceFacilityCRUDIT extends SequenceModuleBaseIT {
+
+  private static final String EXPECTED_NAME = "name";
+  private static final String EXPECTED_GROUP = "DINA GROUP";
+  private static final String EXPECTED_CREATED_BY = "createdBy";
+
+  @Test
+  void create() {
+    SequencingFacility seqFacility = buildExpectedSequenceFacility();
+
+    sequencingFacilityService.create(seqFacility);
+
+    Assertions.assertNotNull(seqFacility.getId());
+    Assertions.assertNotNull(seqFacility.getCreatedOn());
+    Assertions.assertNotNull(seqFacility.getUuid());
+  }
+
+  @Test
+  void find() {
+    SequencingFacility seqFacility = buildExpectedSequenceFacility();
+
+    sequencingFacilityService.create(seqFacility);
+
+    SequencingFacility result = sequencingFacilityService.findOne(seqFacility.getUuid(), SequencingFacility.class);
+
+    Assertions.assertEquals(EXPECTED_NAME, result.getName());
+    Assertions.assertEquals(EXPECTED_GROUP, result.getGroup());
+    Assertions.assertEquals(EXPECTED_CREATED_BY, result.getCreatedBy());
+  }
+
+  private SequencingFacility buildExpectedSequenceFacility() {
+    return SequencingFacilityFactory.newSequencingFacility()
+            .name(EXPECTED_NAME)
+            .group(EXPECTED_GROUP)
+            .createdBy(EXPECTED_CREATED_BY)
+            .build();
+
+  }
+}

src/test/java/ca/gc/aafc/seqdb/api/openapi/SequencingFacilityOpenApiIT.java

@@ -0,0 +1,39 @@
+package ca.gc.aafc.seqdb.api.openapi;
+
+import ca.gc.aafc.dina.testsupport.BaseRestAssuredTest;
+import ca.gc.aafc.dina.testsupport.PostgresTestContainerInitializer;
+import ca.gc.aafc.dina.testsupport.jsonapi.JsonAPITestHelper;
+import ca.gc.aafc.dina.testsupport.specs.OpenAPI3Assertions;
+import ca.gc.aafc.seqdb.api.SeqdbApiLauncher;
+import ca.gc.aafc.seqdb.api.dto.SequencingFacilityDto;
+import ca.gc.aafc.seqdb.api.testsupport.fixtures.SequencingFacilityTestFixture;
+import lombok.SneakyThrows;
+import org.junit.jupiter.api.Test;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.TestPropertySource;
+
+@SpringBootTest(
+        classes = SeqdbApiLauncher.class,
+        webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT
+)
+@TestPropertySource(properties = "spring.config.additional-location=classpath:application-test.yml")
+@ContextConfiguration(initializers = {PostgresTestContainerInitializer.class})
+public class SequencingFacilityOpenApiIT extends BaseRestAssuredTest {
+
+  protected SequencingFacilityOpenApiIT() {
+    super("/api");
+  }
+
+  @SneakyThrows
+  @Test
+  void sequencingFacility_SpecValid() {
+    SequencingFacilityDto sequencingFacility = SequencingFacilityTestFixture.newSequencingFacility();
+
+    OpenAPI3Assertions.assertRemoteSchema(OpenAPIConstants.SEQDB_API_SPECS_URL, "SequencingFacility",
+            sendPost(SequencingFacilityDto.TYPENAME, JsonAPITestHelper.toJsonAPIMap(SequencingFacilityDto.TYPENAME, JsonAPITestHelper.toAttributeMap(sequencingFacility),
+                    null,
+                    null)
+            ).extract().asString());
+  }
+}